mSet_limma: Run linear model with the limma package

In zhuchcn/Metabase: Data container, handling, and visualization for high through-put quantitative experiment data.

Description

This is a function that fits linear models for each single features in a mSet-class object. It calls the function lmFit, followed by eBayes for t tests. The result is returned by topTable. A model matrix is requred to be passed to the lmFit function.

Usage

mSet_limma(object, design, transform = function(x) {     log2(x + 1) },
  coef, p.value)

Arguments

object	A mSet-class object.
design	A design matrix. Can be created using the model.matrix funciton.
transform	A transform function to apply. The defaul is log2 transformation.
coef	The number of coefficient to return by topTable. See topTable.

Value

A data.frame. See topTable

Author(s)

Chenghao Zhu

zhuchcn/Metabase documentation built on July 23, 2019, 1:36 p.m.